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Pushkova EN, Borkhert EV, Novakovskiy RO, Dvorianinova EM, Rozhmina TA, Zhuchenko AA, Zhernova DA, Turba AA, Yablokov AG, Sigova EA, Krasnov GS, Bolsheva NL, Melnikova NV, Dmitriev AA. Selection of Flax Genotypes for Pan-Genomic Studies by Sequencing Tagmentation-Based Transcriptome Libraries. PLANTS (BASEL, SWITZERLAND) 2023; 12:3725. [PMID: 37960081 PMCID: PMC10650069 DOI: 10.3390/plants12213725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023]
Abstract
Flax (Linum usitatissimum L.) products are used in the food, pharmaceutical, textile, polymer, medical, and other industries. The creation of a pan-genome will be an important advance in flax research and breeding. The selection of flax genotypes that sufficiently cover the species diversity is a crucial step for the pan-genomic study. For this purpose, we have adapted a method based on Illumina sequencing of transcriptome libraries prepared using the Tn5 transposase (tagmentase). This approach reduces the cost of sample preparation compared to commercial kits and allows the generation of a large number of cDNA libraries in a short time. RNA-seq data were obtained for 192 flax plants (3-6 individual plants from 44 flax accessions of different morphology and geographical origin). Evaluation of the genetic relationship between flax plants based on the sequencing data revealed incorrect species identification for five accessions. Therefore, these accessions were excluded from the sample set for the pan-genomic study. For the remaining samples, typical genotypes were selected to provide the most comprehensive genetic diversity of flax for pan-genome construction. Thus, high-throughput sequencing of tagmentation-based transcriptome libraries showed high efficiency in assessing the genetic relationship of flax samples and allowed us to select genotypes for the flax pan-genomic analysis.
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Affiliation(s)
- Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Tatiana A. Rozhmina
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
| | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, 115598 Moscow, Russia
| | - Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Anastasia A. Turba
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Arthur G. Yablokov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
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He L, Sui Y, Che Y, Wang H, Rashid KY, Cloutier S, You FM. Genome-wide association studies using multi-models and multi-SNP datasets provide new insights into pasmo resistance in flax. FRONTIERS IN PLANT SCIENCE 2023; 14:1229457. [PMID: 37954993 PMCID: PMC10634603 DOI: 10.3389/fpls.2023.1229457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/24/2023] [Indexed: 11/14/2023]
Abstract
Introduction Flax (Linum usitatissimum L.) is an economically important crop due to its oil and fiber. However, it is prone to various diseases, including pasmo caused by the fungus Septoria linicola. Methods In this study, we conducted field evaluations of 445 flax accessions over a five-year period (2012-2016) to assess their resistance to pasmo A total of 246,035 single nucleotide polymorphisms (SNPs) were used for genetic analysis. Four statistical models, including the single-locus model GEMMA and the multi-locus models FarmCPU, mrMLM, and 3VmrMLM, were assessed to identify quantitative trait nucleotides (QTNs) associated with pasmo resistance. Results We identified 372 significant QTNs or 132 tag QTNs associated with pasmo resistance from five pasmo resistance datasets (PAS2012-PAS2016 and the 5-year average, namely PASmean) and three genotypic datasets (the all SNPs/ALL, the gene-based SNPs/GB and the RGA-based SNPs/RGAB). The tag QTNs had R2 values of 0.66-16.98% from the ALL SNP dataset, 0.68-20.54%from the GB SNP dataset, and 0.52-22.42% from the RGAB SNP dataset. Of these tag QTNs, 93 were novel. Additionally, 37 resistance gene analogs (RGAs)co-localizing with 39 tag QTNs were considered as potential candidates for controlling pasmo resistance in flax and 50 QTN-by-environment interactions(QEIs) were identified to account for genes by environmental interactions. Nine RGAs were predicted as candidate genes for ten QEIs. Discussion Our results suggest that pasmo resistance in flax is polygenic and potentially influenced by environmental factors. The identified QTNs provide potential targets for improving pasmo resistance in flax breeding programs. This study sheds light on the genetic basis of pasmo resistance and highlights the importance of considering both genetic and environmental factors in breeding programs for flax.
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Affiliation(s)
- Liqiang He
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Yao Sui
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Yanru Che
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Huixian Wang
- School of Tropical Agriculture and Forestry, School of Tropical Crops, Hainan University, Haikou, China
| | - Khalid Y. Rashid
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
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Moyse J, Lecomte S, Marcou S, Mongelard G, Gutierrez L, Höfte M. Overview and Management of the Most Common Eukaryotic Diseases of Flax ( Linum usitatissimum). PLANTS (BASEL, SWITZERLAND) 2023; 12:2811. [PMID: 37570965 PMCID: PMC10420651 DOI: 10.3390/plants12152811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023]
Abstract
Flax is an important crop cultivated for its seeds and fibers. It is widely grown in temperate regions, with an increase in cultivation areas for seed production (linseed) in the past 50 years and for fiber production (fiber flax) in the last decade. Among fiber-producing crops, fiber flax is the most valuable species. Linseed is the highest omega-3 oleaginous crop, and its consumption provides several benefits for animal and human health. However, flax production is impacted by various abiotic and biotic factors that affect yield and quality. Among biotic factors, eukaryotic diseases pose a significant threat to both seed production and fiber quality, which highlights the economic importance of controlling these diseases. This review focuses on the major eukaryotic diseases that affect flax in the field, describing the pathogens, their transmission modes and the associated plant symptoms. Moreover, this article aims to identify the challenges in disease management and provide future perspectives to overcome these biotic stresses in flax cultivation. By emphasizing the key diseases and their management, this review can aid in promoting sustainable and profitable flax production.
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Affiliation(s)
- Julie Moyse
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure Links 653, 9000 Ghent, Belgium; (J.M.); (S.M.)
- Centre de Ressources Régionales en Biologie Moléculaire, University of Picardie Jules Verne, UFR Sciences, 33 Rue St-Leu, 80039 Amiens, France;
| | - Sylvain Lecomte
- LINEA–Semences, 20 Avenue Saget, 60210 Grandvilliers, France;
| | - Shirley Marcou
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure Links 653, 9000 Ghent, Belgium; (J.M.); (S.M.)
| | - Gaëlle Mongelard
- Centre de Ressources Régionales en Biologie Moléculaire, University of Picardie Jules Verne, UFR Sciences, 33 Rue St-Leu, 80039 Amiens, France;
| | - Laurent Gutierrez
- Centre de Ressources Régionales en Biologie Moléculaire, University of Picardie Jules Verne, UFR Sciences, 33 Rue St-Leu, 80039 Amiens, France;
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure Links 653, 9000 Ghent, Belgium; (J.M.); (S.M.)
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Paliwal S, Tripathi MK, Tiwari S, Tripathi N, Payasi DK, Tiwari PN, Singh K, Yadav RK, Asati R, Chauhan S. Molecular Advances to Combat Different Biotic and Abiotic Stresses in Linseed ( Linum usitatissimum L.): A Comprehensive Review. Genes (Basel) 2023; 14:1461. [PMID: 37510365 PMCID: PMC10379177 DOI: 10.3390/genes14071461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Flax, or linseed, is considered a "superfood", which means that it is a food with diverse health benefits and potentially useful bioactive ingredients. It is a multi-purpose crop that is prized for its seed oil, fibre, nutraceutical, and probiotic qualities. It is suited to various habitats and agro-ecological conditions. Numerous abiotic and biotic stressors that can either have a direct or indirect impact on plant health are experienced by flax plants as a result of changing environmental circumstances. Research on the impact of various stresses and their possible ameliorators is prompted by such expectations. By inducing the loss of specific alleles and using a limited number of selected varieties, modern breeding techniques have decreased the overall genetic variability required for climate-smart agriculture. However, gene banks have well-managed collectionns of landraces, wild linseed accessions, and auxiliary Linum species that serve as an important source of novel alleles. In the past, flax-breeding techniques were prioritised, preserving high yield with other essential traits. Applications of molecular markers in modern breeding have made it easy to identify quantitative trait loci (QTLs) for various agronomic characteristics. The genetic diversity of linseed species and the evaluation of their tolerance to abiotic stresses, including drought, salinity, heavy metal tolerance, and temperature, as well as resistance to biotic stress factors, viz., rust, wilt, powdery mildew, and alternaria blight, despite addressing various morphotypes and the value of linseed as a supplement, are the primary topics of this review.
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Affiliation(s)
- Shruti Paliwal
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Manoj Kumar Tripathi
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Sushma Tiwari
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur 482004, India
| | - Devendra K Payasi
- All India Coordinated Research Project on Linseed, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Regional Agricultural Research Station, Sagar 470001, India
| | - Prakash N Tiwari
- Department of Plant Molecular Biology and Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Kirti Singh
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Rakesh Kumar Yadav
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Ruchi Asati
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Shailja Chauhan
- Department of Genetics and Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
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Kaur V, Singh M, Wankhede DP, Gupta K, Langyan S, Aravind J, Thangavel B, Yadav SK, Kalia S, Singh K, Kumar A. Diversity of Linum genetic resources in global genebanks: from agro-morphological characterisation to novel genomic technologies - a review. Front Nutr 2023; 10:1165580. [PMID: 37324736 PMCID: PMC10267467 DOI: 10.3389/fnut.2023.1165580] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/27/2023] [Indexed: 06/17/2023] Open
Abstract
Linseed or flaxseed is a well-recognized nutritional food with nutraceutical properties owing to high omega-3 fatty acid (α-Linolenic acid), dietary fiber, quality protein, and lignan content. Currently, linseed enjoys the status of a 'superfood' and its integration in the food chain as a functional food is evolving continuously as seed constituents are associated with lowering the risk of chronic ailments, such as heart diseases, cancer, diabetes, and rheumatoid arthritis. This crop also receives much attention in the handloom and textile sectors as the world's coolest fabric linen is made up of its stem fibers which are endowed with unique qualities such as luster, tensile strength, density, bio-degradability, and non-hazardous nature. Worldwide, major linseed growing areas are facing erratic rainfall and temperature patterns affecting flax yield, quality, and response to biotic stresses. Amid such changing climatic regimes and associated future threats, diverse linseed genetic resources would be crucial for developing cultivars with a broad genetic base for sustainable production. Furthermore, linseed is grown across the world in varied agro-climatic conditions; therefore it is vital to develop niche-specific cultivars to cater to diverse needs and keep pace with rising demands globally. Linseed genetic diversity conserved in global genebanks in the form of germplasm collection from natural diversity rich areas is expected to harbor genetic variants and thus form crucial resources for breeding tailored crops to specific culinary and industrial uses. Global genebank collections thus potentially play an important role in supporting sustainable agriculture and food security. Currently, approximately 61,000 germplasm accessions of linseed including 1,127 wild accessions are conserved in genebanks/institutes worldwide. This review analyzes the current status of Linum genetic resources in global genebanks, evaluation for agro-morphological traits, stress tolerance, and nutritional profiling to promote their effective use for sustainable production and nutrition enhancement in our modern diets.
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Affiliation(s)
- Vikender Kaur
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Mamta Singh
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Dhammaprakash Pandhari Wankhede
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kavita Gupta
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sapna Langyan
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Jayaraman Aravind
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Boopathi Thangavel
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Shashank Kumar Yadav
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kalia
- Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi, India
| | - Kuldeep Singh
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ashok Kumar
- Division of Germplasm Evaluation, Indian Council of Agricultural Research-National Bureau of Plant Genetic Resources, New Delhi, India
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Yadav B, Kaur V, Narayan OP, Yadav SK, Kumar A, Wankhede DP. Integrated omics approaches for flax improvement under abiotic and biotic stress: Current status and future prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:931275. [PMID: 35958216 PMCID: PMC9358615 DOI: 10.3389/fpls.2022.931275] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 05/03/2023]
Abstract
Flax (Linum usitatissimum L.) or linseed is one of the important industrial crops grown all over the world for seed oil and fiber. Besides oil and fiber, flax offers a wide range of nutritional and therapeutic applications as a feed and food source owing to high amount of α-linolenic acid (omega-3 fatty acid), lignans, protein, minerals, and vitamins. Periodic losses caused by unpredictable environmental stresses such as drought, heat, salinity-alkalinity, and diseases pose a threat to meet the rising market demand. Furthermore, these abiotic and biotic stressors have a negative impact on biological diversity and quality of oil/fiber. Therefore, understanding the interaction of genetic and environmental factors in stress tolerance mechanism and identification of underlying genes for economically important traits is critical for flax improvement and sustainability. In recent technological era, numerous omics techniques such as genomics, transcriptomics, metabolomics, proteomics, phenomics, and ionomics have evolved. The advancements in sequencing technologies accelerated development of genomic resources which facilitated finer genetic mapping, quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection in major cereal and oilseed crops including flax. Extensive studies in the area of genomics and transcriptomics have been conducted post flax genome sequencing. Interestingly, research has been focused more for abiotic stresses tolerance compared to disease resistance in flax through transcriptomics, while the other areas of omics such as metabolomics, proteomics, ionomics, and phenomics are in the initial stages in flax and several key questions remain unanswered. Little has been explored in the integration of omic-scale data to explain complex genetic, physiological and biochemical basis of stress tolerance in flax. In this review, the current status of various omics approaches for elucidation of molecular pathways underlying abiotic and biotic stress tolerance in flax have been presented and the importance of integrated omics technologies in future research and breeding have been emphasized to ensure sustainable yield in challenging environments.
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Affiliation(s)
- Bindu Yadav
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Vikender Kaur
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Om Prakash Narayan
- College of Arts and Sciences, University of Florida, Gainesville, FL, United States
| | - Shashank Kumar Yadav
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ashok Kumar
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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Speck A, Trouvé JP, Enjalbert J, Geffroy V, Joets J, Moreau L. Genetic Architecture of Powdery Mildew Resistance Revealed by a Genome-Wide Association Study of a Worldwide Collection of Flax ( Linum usitatissimum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:871633. [PMID: 35812909 PMCID: PMC9263915 DOI: 10.3389/fpls.2022.871633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Powdery mildew is one of the most important diseases of flax and is particularly prejudicial to its yield and oil or fiber quality. This disease, caused by the obligate biotrophic ascomycete Oïdium lini, is progressing in France. Genetic resistance of varieties is critical for the control of this disease, but very few resistance genes have been identified so far. It is therefore necessary to identify new resistance genes to powdery mildew suitable to the local context of pathogenicity. For this purpose, we studied a worldwide diversity panel composed of 311 flax genotypes both phenotyped for resistance to powdery mildew resistance over 2 years of field trials in France and resequenced. Sequence reads were mapped on the CDC Bethune reference genome revealing 1,693,910 high-quality SNPs, further used for both population structure analysis and genome-wide association studies (GWASs). A number of four major genetic groups were identified, separating oil flax accessions from America or Europe and those from Asia or Middle-East and fiber flax accessions originating from Eastern Europe and those from Western Europe. A number of eight QTLs were detected at the false discovery rate threshold of 5%, located on chromosomes 1, 2, 4, 13, and 14. Taking advantage of the moderate linkage disequilibrium present in the flax panel, and using the available genome annotation, we identified potential candidate genes. Our study shows the existence of new resistance alleles against powdery mildew in our diversity panel, of high interest for flax breeding program.
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Affiliation(s)
| | | | - Jérôme Enjalbert
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution - Le Moulon, Gif-sur-Yvette, France
| | - Valérie Geffroy
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Johann Joets
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution - Le Moulon, Gif-sur-Yvette, France
| | - Laurence Moreau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution - Le Moulon, Gif-sur-Yvette, France
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Saroha A, Pal D, Gomashe SS, Akash, Kaur V, Ujjainwal S, Rajkumar S, Aravind J, Radhamani J, Kumar R, Chand D, Sengupta A, Wankhede DP. Identification of QTNs Associated With Flowering Time, Maturity, and Plant Height Traits in Linum usitatissimum L. Using Genome-Wide Association Study. Front Genet 2022; 13:811924. [PMID: 35774513 PMCID: PMC9237403 DOI: 10.3389/fgene.2022.811924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/02/2022] [Indexed: 12/21/2022] Open
Abstract
Early flowering, maturity, and plant height are important traits for linseed to fit in rice fallows, for rainfed agriculture, and for economically viable cultivation. Here, Multi-Locus Genome-Wide Association Study (ML-GWAS) was undertaken in an association mapping panel of 131 accessions, genotyped using 68,925 SNPs identified by genotyping by sequencing approach. Phenotypic evaluation data of five environments comprising 3 years and two locations were used. GWAS was performed for three flowering time traits including days to 5%, 50%, and 95% flowering, days to maturity, and plant height by employing five ML-GWAS methods: FASTmrEMMA, FASTmrMLM, ISIS EM-BLASSO, mrMLM, and pLARmEB. A total of 335 unique QTNs have been identified for five traits across five environments. 109 QTNs were stable as observed in ≥2 methods and/or environments, explaining up to 36.6% phenotypic variance. For three flowering time traits, days to maturity, and plant height, 53, 30, and 27 stable QTNs, respectively, were identified. Candidate genes having roles in flower, pollen, embryo, seed and fruit development, and xylem/phloem histogenesis have been identified. Gene expression of candidate genes for flowering and plant height were studied using transcriptome of an early maturing variety Sharda (IC0523807). The present study unravels QTNs/candidate genes underlying complex flowering, days to maturity, and plant height traits in linseed.
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You FM, Rashid KY, Zheng C, Khan N, Li P, Xiao J, He L, Yao Z, Cloutier S. Insights into the Genetic Architecture and Genomic Prediction of Powdery Mildew Resistance in Flax ( Linum usitatissimum L.). Int J Mol Sci 2022; 23:ijms23094960. [PMID: 35563347 PMCID: PMC9104541 DOI: 10.3390/ijms23094960] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 12/29/2022] Open
Abstract
Powdery mildew (PM), caused by the fungus Oidium lini in flax, can cause defoliation and reduce seed yield and quality. To date, one major dominant gene (Pm1) and three quantitative trait loci (QTL) on chromosomes 1, 7 and 9 have been reported for PM resistance. To fully dissect the genetic architecture of PM resistance and identify QTL, a diverse flax core collection of 372 accessions augmented with an additional 75 breeding lines were sequenced, and PM resistance was evaluated in the field for eight years (2010–2017) in Morden, Manitoba, Canada. Genome-wide association studies (GWAS) were performed using two single-locus and seven multi-locus statistical models with 247,160 single nucleotide polymorphisms (SNPs) and the phenotypes of the 447 individuals for each year separately as well as the means over years. A total of 349 quantitative trait nucleotides (QTNs) were identified, of which 44 large-effect QTNs (R2 = 10–30%) were highly stable over years. The total number of favourable alleles per accession was significantly correlated with PM resistance (r = 0.74), and genomic selection (GS) models using all identified QTNs generated significantly higher predictive ability (r = 0.93) than those constructed using the 247,160 genome-wide random SNP (r = 0.69), validating the overall reliability of the QTNs and showing the additivity of PM resistance in flax. The QTNs were clustered on the distal ends of all 15 chromosomes, especially on chromosome 5 (0.4–5.6 Mb and 9.4–16.9 Mb) and 13 (4.7–5.2 Mb). To identify candidate genes, a dataset of 3230 SNPs located in resistance gene analogues (RGAs) was used as input for GWAS, from which an additional 39 RGA-specific QTNs were identified. Overall, 269 QTN loci harboured 445 RGAs within the 200 Kb regions spanning the QTNs, including 45 QTNs located within the RGAs. These RGAs supported by significant QTN/SNP allele effects were mostly nucleotide binding site and leucine-rich repeat receptors (NLRs) belonging to either coiled-coil (CC) NLR (CNL) or toll interleukin-1 (TIR) NLR (TNL), receptor-like kinase (RLK), receptor-like protein kinase (RLP), transmembrane-coiled-coil (TM-CC), WRKY, and mildew locus O (MLO) genes. These results constitute an important genomic tool for resistance breeding and gene cloning for PM in flax.
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Affiliation(s)
- Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Correspondence: (F.M.Y.); (S.C.); Tel.: +1-613-759-1539 (F.M.Y.); +1-613-759-1744 (S.C.)
| | - Khalid Y. Rashid
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (K.Y.R.); (Z.Y.)
| | - Chunfang Zheng
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
| | - Nadeem Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Pingchuan Li
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
| | - Jin Xiao
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China;
| | - Liqiang He
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing 210095, China;
| | - Zhen Yao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada; (K.Y.R.); (Z.Y.)
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (C.Z.); (N.K.); (P.L.); (L.H.)
- Correspondence: (F.M.Y.); (S.C.); Tel.: +1-613-759-1539 (F.M.Y.); +1-613-759-1744 (S.C.)
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Duk M, Kanapin A, Samsonova A, Rozhmina T, Samsonova M. Analysis of Structural Variation in Flax (Linum usitatissimum L.) Genomes. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922020038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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11
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Duk M, Kanapin A, Rozhmina T, Bankin M, Surkova S, Samsonova A, Samsonova M. The Genetic Landscape of Fiber Flax. FRONTIERS IN PLANT SCIENCE 2021; 12:764612. [PMID: 34950165 PMCID: PMC8691122 DOI: 10.3389/fpls.2021.764612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
Genetic diversity in a breeding program is essential to overcome modern-day environmental challenges faced by humanity and produce robust, resilient crop cultivars with improved agronomic characteristics, as well as to trace crop domestication history. Flax (Linum usitatissimum), one of the first crops domesticated by mankind, has been traditionally cultivated for fiber as well as for medicinal purposes and as a nutritional product. The origins of fiber flax are hidden in the mists of time and can be hypothetically traced back to either the Indo-Afghan region or Fertile Crescent. To shed new light on fiber flax genetic diversity and breeding history, in this study, we presented a comprehensive analysis of the core collection of flax (306 accessions) of different morphotypes and geographic origins maintained by the Russian Federal Research Center for Bast Fiber Crops. We observed significant population differentiation between oilseed and fiber morphotypes, as well as mapped genomic regions affected by recent breeding efforts. We also sought to unravel the origins of kryazhs, Russian heritage landraces, and their genetic relatedness to modern fiber flax cultivars. For the first time, our results provide strong genetic evidence in favor of the hypothesis on kryazh's mixed origin from both the Indo-Afghan diversity center and Fertile Crescent. Finally, we showed predominant contribution from Russian landraces and kryazhs into the ancestry of modern fiber flax varieties. Taken together, these findings may have practical implications on the development of new improved flax varieties with desirable traits that give farmers greater choice in crop management and meet the aspirations of breeders.
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Affiliation(s)
- Maria Duk
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Alexander Kanapin
- Centre for Computational Biology, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Tatyana Rozhmina
- Laboratory of Breeding Technologies, Federal Research Center for Bast Fiber Crops, Torzhok, Russia
| | - Mikhail Bankin
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Svetlana Surkova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Anastasia Samsonova
- Centre for Computational Biology, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Maria Samsonova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
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12
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Van Pamel E, Cnops G, Van Droogenbroeck B, Delezie EC, Van Royen G, Vlaemynck GM, Aper J, Muylle H, Bekaert KM, Cooreman K, Robbens J, Delbare D, Roldan-Ruiz I, Crivits M, De Ruyck H, Herman L. Opportunities within the Agri-food System to Encourage a Nutritionally Balanced Diet – Part I. FOOD REVIEWS INTERNATIONAL 2021. [DOI: 10.1080/87559129.2020.1719504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Els Van Pamel
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Melle, Belgium
| | - Gerda Cnops
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
| | - Bart Van Droogenbroeck
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Melle, Belgium
| | - Evelyne C. Delezie
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Animal Sciences Unit, Melle, Belgium
| | - Geert Van Royen
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Melle, Belgium
| | - Geertrui Mml Vlaemynck
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Melle, Belgium
| | - Jonas Aper
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
| | - Hilde Muylle
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
| | - Karen Mm Bekaert
- Flanders Research Institute for Agriculture Fisheries and Food (ILVO), Animal Sciences Unit, Oostende, Belgium
| | - Kris Cooreman
- Flanders Research Institute for Agriculture Fisheries and Food (ILVO), Animal Sciences Unit, Oostende, Belgium
| | - Johan Robbens
- Flanders Research Institute for Agriculture Fisheries and Food (ILVO), Animal Sciences Unit, Oostende, Belgium
| | - Daan Delbare
- Flanders Research Institute for Agriculture Fisheries and Food (ILVO), Animal Sciences Unit, Oostende, Belgium
| | - Isabel Roldan-Ruiz
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences Unit, Melle, Belgium
| | - Maarten Crivits
- Flanders Research Institute for Agriculture Fisheries and Food (ILVO), Social Sciences Unit, Merelbeke, Belgium
| | - Hendrik De Ruyck
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Melle, Belgium
| | - Lieve Herman
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Melle, Belgium
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13
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Sertse D, You FM, Ravichandran S, Soto-Cerda BJ, Duguid S, Cloutier S. Loci harboring genes with important role in drought and related abiotic stress responses in flax revealed by multiple GWAS models. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:191-212. [PMID: 33047220 DOI: 10.1007/s00122-020-03691-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 09/18/2020] [Indexed: 05/19/2023]
Abstract
QTNs associated with drought tolerance traits and indices were identified in a flax mini-core collection through multiple GWAS models and phenotyping at multiple locations under irrigated and non-irrigated field conditions. Drought is a critical phenomenon challenging today's agricultural sector. Crop varieties adapted to moisture deficit are becoming vital. Flax can be greatly affected by limiting moisture conditions, especially during the early development and reproductive stages. Here, a mini-core collection comprising genotypes from more than 20 major growing countries was evaluated for 11 drought-related traits in irrigated and non-irrigated fields for 3 years. Heritability of the traits ranged from 44.7 to 86%. Six of the 11 traits showed significant phenotypic difference between irrigated and non-irrigated conditions. A genome-wide association study (GWAS) was performed for these six traits and their corresponding stress indices based on 106 genotypes and 12,316 single nucleotide polymorphisms (SNPs) using six multi-locus and one single-locus models. The SNPs were then assigned to 8050 linkage disequilibrium (LD) blocks to which a restricted two-stage multi-locus multi-allele GWAS was applied. A total of 144 quantitative trait nucleotides (QTNs) and 13 LD blocks were associated with at least one trait or stress index. Of these, 16 explained more than 15% of the genetic variance. Most large-effect QTN loci harbored gene(s) previously predicted to play role(s) in the associated traits. Genes mediating responses to abiotic stresses resided at loci associated with stress indices. Flax genes Lus10009480 and Lus10030150 that are predicted to encode WAX INDUCER1 and STRESS-ASSOCIATED PROTEIN (SAP), respectively, are among the important candidates detected. Accessions with multiple favorable alleles outperformed others for grain yield, thousand seed weight and fiber/biomass in non-irrigated conditions, suggesting their potential usefulness in breeding and genomic selection.
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Affiliation(s)
- Demissew Sertse
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada
| | - Sridhar Ravichandran
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada
| | - Braulio J Soto-Cerda
- Agriaquaculture Nutritional Genomic Centre (CGNA), Las Heras 350, 4781158, Temuco, Chile
| | - Scott Duguid
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, Canada
| | - Sylvie Cloutier
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON, Canada.
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, Canada.
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14
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New insights on the function of plant acyl carrier proteins from comparative and evolutionary analysis. Genomics 2020; 113:1155-1165. [PMID: 33221517 DOI: 10.1016/j.ygeno.2020.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/02/2020] [Accepted: 11/16/2020] [Indexed: 11/20/2022]
Abstract
Acyl carrier proteins (ACPs) play a central role in both plastidial and mitochondrial Type II fatty acid synthesis in plant cells. However, a large proportion of plant ACPs remain functionally uncharacterized, and their evolutionary history remains elusive. In present study, 97 putative ACPs were identified from ten angiosperm species examined. Based on phylogenetic analysis, ACP genes were grouped into plastidial (cpACP: ACP1/2/3/4/5) and mitochondrial (mtACP: mtACP1/mtACP2/mtACP3) ACPs. Protein sequence (motifs and length), tertiary structure, and gene structure (exon number, average intron length, and intron phase) were highly conserved in different ACP subclades. The differentiation of ACPs into distinct types occurred 85-98 and 45-57 million years ago. A limited proportion of ACP genes experience tandem or segmental duplication, corresponding to two rounds of whole genome duplication. Ka/Ks ratios revealed that duplicated ACP genes underwent a purifying selection. Regarding expression patterns, most ACPs were expressed constitutively and tissue-specifically. Notably, the average expression levels of ACP1, mtACP3, and mtACP1 were positively correlated with those of ACP3, ACP4, and mtACP2, respectively. Analysis of cis-elements showed that seven motifs (CACTFTPPCA1, DOFCOREZM, GT1CONSENSUS, CAATBOX1, ARR1AT, POLLEN1LELAT52, and GATABOX) related to tissue-specific, ABA, and light-mediated gene regulation were ubiquitous in all ACPs investigated, which shed new light on the regulation patterns of these central enzymatic partners of the FAS system. This study presents a thorough overview of angiosperm ACP gene families and provides informative clues for the functional characterization of plant ACPs in the future.
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Hoque A, Fiedler JD, Rahman M. Genetic diversity analysis of a flax (Linum usitatissimum L.) global collection. BMC Genomics 2020; 21:557. [PMID: 32795254 PMCID: PMC7430851 DOI: 10.1186/s12864-020-06922-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/17/2020] [Indexed: 11/25/2022] Open
Abstract
Background A sustainable breeding program requires a minimum level of germplasm diversity to provide varied options for the selection of new breeding lines. To maximize genetic gain of the North Dakota State University (NDSU) flax breeding program, we aimed to increase the genetic diversity of its parental stocks by incorporating diverse genotypes. For this purpose, we analyzed the genetic diversity, linkage disequilibrium, and population sub-structure of 350 globally-distributed flax genotypes with 6200 SNP markers. Results All the genotypes tested clustered into seven sub-populations (P1 to P7) based on the admixture model and the output of neighbor-joining (NJ) tree analysis and principal coordinate analysis were in line with that of structure analysis. The largest sub-population separation arose from a cluster of NDSU/American genotypes with Turkish and Asian genotypes. All sub-populations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise Fst comparison revealed a great degree of divergence (Fst > 0.25) between most of the combinations. A whole collection mantel test showed significant positive correlation (r = 0.30 and p < 0.01) between genetic and geographic distances, whereas it was non-significant for all sub-populations except P4 and P5 (r = 0.251, 0.349 respectively and p < 0.05). In the entire collection, the mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 21 kb distance. Conclusions To maximize genetic gain, hybridization between NDSU stock (P5) and Asian individuals (P6) are potentially the best option as genetic differentiation between them is highest (Fst > 0.50). In contrast, low genetic differentiation between P5 and P2 may enhance the accumulation of favorable alleles for oil and fiber upon crossing to develop dual purpose varieties. As each sub-population consists of many genotypes, a Neighbor-Joining tree and kinship matrix assist to identify distantly related genotypes. These results also inform genotyping decisions for future association mapping studies to ensure the identification of a sufficient number of molecular markers to tag all linkage blocks.
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Affiliation(s)
- Ahasanul Hoque
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Jason D Fiedler
- Cereal Crops Research, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, USA
| | - Mukhlesur Rahman
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA.
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16
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Guo D, Jiang H, Yan W, Yang L, Ye J, Wang Y, Yan Q, Chen J, Gao Y, Duan L, Liu H, Xie L. Resequencing 200 Flax Cultivated Accessions Identifies Candidate Genes Related to Seed Size and Weight and Reveals Signatures of Artificial Selection. FRONTIERS IN PLANT SCIENCE 2020; 10:1682. [PMID: 32010166 PMCID: PMC6976528 DOI: 10.3389/fpls.2019.01682] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/29/2019] [Indexed: 05/13/2023]
Abstract
Seed size and weight are key traits determining crop yield, which often undergo strongly artificial selection during crop domestication. Although seed sizes differ significantly between oil flax and fiber flax, the genetic basis of morphological differences and artificial selection characteristics in seed size remains largely unclear. Here we re-sequenced 200 flax cultivated accessions to generate a genome variation map based on chromosome assembly reference genomes. We provide evidence that oil flax group is the ancestor of cultivated flax, and the oil-fiber dual purpose group (OF) is the evolutionary intermediate transition state between oil and fiber flax. Genome-wide association studies (GWAS) were combined with LD Heatmap to identify candidate regions related to seed size and weight, then candidate genes were screened based on detailed functional annotations and estimation of nucleotide polymorphism effects. Using this strategy, we obtained 13 candidate genes related to seed size and weight. Selective sweeps analysis indicates human-involved selection of small seeds during the oil to fiber flax transition. Our study shows the existence of elite alleles for seed size and weight in flax germplasm and provides molecular insights into approaches for further improvement.
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Affiliation(s)
- Dongliang Guo
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Haixia Jiang
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Wenliang Yan
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Liangjie Yang
- Herbal Medicine Innovation Research Center, Agricultural Bureau of Zhaosu County, Yili, China
| | - Jiali Ye
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Yue Wang
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Qingcheng Yan
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Jiaxun Chen
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Yanfang Gao
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Lepeng Duan
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Huiqing Liu
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Liqiong Xie
- National Center of Melon Engineering and Technology, Molecular Breeding Laboratory, College of Life Science and Technology, Xinjiang University, Urumqi, China
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Sertse D, You FM, Ravichandran S, Cloutier S. The Complex Genetic Architecture of Early Root and Shoot Traits in Flax Revealed by Genome-Wide Association Analyses. FRONTIERS IN PLANT SCIENCE 2019; 10:1483. [PMID: 31798617 PMCID: PMC6878218 DOI: 10.3389/fpls.2019.01483] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/25/2019] [Indexed: 05/05/2023]
Abstract
Roots are fundamental organs for water and nutrient uptake as well as for signal transduction in response to biotic and abiotic stresses. Flax has a shallow tap root system that relies mostly on top soil nutrient and moisture resources. The crop can easily be outcompeted by weeds or other crops in intercropping systems, especially in moisture deficit conditions. However, there is a wide range of variation among genotypes in terms of performance under scarce resources such as moisture limitation. Here we phenotyped 15 root, two shoot traits and shoot to root dry weight ratio on 115 flax accessions grown in a hydroponic pouch system and performed a genome-wide association study (GWAS) based on seven different models to identify quantitative trait loci underlying these traits. Significant variation among genotypes was observed for the two shoot and 12 of the 14 root traits. Shoot dry weight was correlated with root network volume, length, surface area, and root dry weight (r > 0.5, P < 0.001) but not significantly correlated with root depth (r = 0.033, P > 0.05). The seven GWAS models detected a total of 228 quantitative trait nucleotides (QTNs) for 16 traits. Most loci, defined by an interval of 100 kb up and downstream of the QTNs, harbored genes known to play role(s) in root and shoot development, suggesting them as candidates. Examples of candidate genes linked to root network QTNs included genes encoding GRAS transcription factors, mitogen-activated protein kinases, and auxin related lateral organ boundary proteins while QTN loci for shoot dry weight harbored genes involved in photomorphogenesis and plant immunity. These results provide insights into the genetic bases of early shoot and root development traits in flax that could be capitalized upon to improve its root architecture, particularly in view of better withstanding water limiting conditions during the cropping season.
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Affiliation(s)
- Demissew Sertse
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Frank M. You
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sridhar Ravichandran
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
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18
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Sertse D, You FM, Ravichandran S, Cloutier S. The genetic structure of flax illustrates environmental and anthropogenic selections that gave rise to its eco-geographical adaptation. Mol Phylogenet Evol 2019; 137:22-32. [PMID: 30978393 DOI: 10.1016/j.ympev.2019.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 04/06/2019] [Accepted: 04/08/2019] [Indexed: 01/15/2023]
Abstract
Flax, one of the eight founder crops of agriculture, has been cultivated for its oil and/or fiber for millennia. Understanding genetic divergence and geographic origins of germplasm in line with their cultivation history and ecological adaptation are essential for conservation and breeding. Here we performed a genome-wide assessment based on more than 51,000 single nucleotide polymorphic sites defining 383 flax accessions from a core collection representing 37 flax growing countries. Population structure analysis resulted in a total of 12 populations that were pooled into four major groups: Temperate, South Asian, Abyssinian and Mediterranean. The vast majority (n = 335) belonged to the Temperate group that comprised eight populations including one dominated by fiber flax. Genetic variation between fiber and oil morphotypes was less pronounced than variation within morphotypes. The genetic variation among groups and populations was attributed in part to eco-geographic and anthropogenic factors. Genetic signatures indicated loci under strong selection by environmental factors such as day length. A high concentration of private haplotypes were observed in the South Asian, Mediterranean and Abyssinian populations despite their low genotype representation, hinting at the long history of the crop in these regions. The addition of genotypes from these three regions would enrich the core collection by capturing a wider genetic breadth for breeding and conservation.
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Affiliation(s)
- Demissew Sertse
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada; Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Frank M You
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Sridhar Ravichandran
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A 0C6, Canada; Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada.
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Flax latitudinal adaptation at LuTFL1 altered architecture and promoted fiber production. Sci Rep 2019; 9:976. [PMID: 30700760 PMCID: PMC6354013 DOI: 10.1038/s41598-018-37086-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 11/02/2018] [Indexed: 01/30/2023] Open
Abstract
After domestication in the Near East around 10,000 years ago several founder crops, flax included, spread to European latitudes. On reaching northerly latitudes the architecture of domesticated flax became more suitable to fiber production over oil, with longer stems, smaller seeds and fewer axillary branches. Latitudinal adaptations in crops typically result in changes in flowering time, often involving the PEBP family of genes that also have the potential to influence plant architecture. Two PEBP family genes in the flax genome, LuTFL1 and LuTFL2, vary in wild and cultivated flax over latitudinal range with cultivated flax receiving LuTFL1 alleles from northerly wild flax populations. Compared to a background of population structure of flaxes over latitude, the LuTFL1 alleles display a level of differentiation that is consistent with selection for an allele III in the north. We demonstrate through heterologous expression in Arabidopsis thaliana that LuTFL1 is a functional homolog of TFL1 in A. thaliana capable of changing both flowering time and plant architecture. We conclude that specialized fiber flax types could have formed as a consequence of a natural adaptation of cultivated flax to higher latitudes.
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He L, Xiao J, Rashid KY, Yao Z, Li P, Jia G, Wang X, Cloutier S, You FM. Genome-Wide Association Studies for Pasmo Resistance in Flax ( Linum usitatissimum L.). FRONTIERS IN PLANT SCIENCE 2019; 9:1982. [PMID: 30693010 PMCID: PMC6339956 DOI: 10.3389/fpls.2018.01982] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 12/20/2018] [Indexed: 05/04/2023]
Abstract
Pasmo is one of the most widespread diseases threatening flax production. To identify genetic regions associated with pasmo resistance (PR), a genome-wide association study was performed on 370 accessions from the flax core collection. Evaluation of pasmo severity was performed in the field from 2012 to 2016 in Morden, MB, Canada. Genotyping-by-sequencing has identified 258,873 single nucleotide polymorphisms (SNPs) distributed on all 15 flax chromosomes. Marker-trait associations were identified using ten different statistical models. A total of 692 unique quantitative trait nucleotides (QTNs) associated with 500 putative quantitative trait loci (QTL) were detected from six phenotypic PR datasets (five individual years and average across years). Different QTNs were identified with various statistical models and from individual PR datasets, indicative of the complementation between analytical methods and/or genotype × environment interactions of the QTL effects. The single-locus models tended to identify large-effect QTNs while the multi-loci models were able to detect QTNs with smaller effects. Among the putative QTL, 67 had large effects (3-23%), were stable across all datasets and explained 32-64% of the total variation for PR in the various datasets. Forty-five of these QTL spanned 85 resistance gene analogs including a large toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (TNL) type gene cluster on chromosome 8. The number of QTL with positive-effect or favorite alleles (NPQTL) in accessions was significantly correlated with PR (R 2 = 0.55), suggesting that these QTL effects are mainly additive. NPQTL was also significantly associated with morphotype (R 2 = 0.52) and major QTL with positive effect alleles were present in the fiber type accessions. The 67 large effect QTL are suited for marker-assisted selection and the 500 QTL for effective genomic prediction in PR molecular breeding.
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Affiliation(s)
- Liqiang He
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - Jin Xiao
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - Khalid Y. Rashid
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Zhen Yao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Pingchuan Li
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Gaofeng Jia
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Xiue Wang
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Frank M. You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
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Saha D, Rana RS, Das S, Datta S, Mitra J, Cloutier SJ, You FM. Genome-wide regulatory gene-derived SSRs reveal genetic differentiation and population structure in fiber flax genotypes. J Appl Genet 2018; 60:13-25. [PMID: 30368734 DOI: 10.1007/s13353-018-0476-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 10/13/2018] [Accepted: 10/16/2018] [Indexed: 01/06/2023]
Abstract
We designed a set of 580 simple sequence repeat markers; 506 from transcription factor-coding genes, and 74 from long non-coding RNAs and designated them as regulatory gene-derived simple sequence repeat (ReG-SSR) markers. From this set, we could anchor 559 ReG-SSR markers on 15 flax chromosomes with an average marker distance of 0.56 Mb. Thirty-one polymorphic ReG-SSR primers, amplifying SSR loci length of at least 20 bp were chosen from 134 screened primers. This primer set was used to characterize a diversity panel of 93 flax accessions. The panel included 33 accessions from India, including released varieties, dual-purpose lines and landraces, and 60 fiber flax accessions from the global core collection. Thirty-one ReG-SSR markers generated 76 alleles, with an average of 2.5 alleles per primer and a mean allele frequency of 0.77. These markers recorded 0.32 average gene diversity, 0.26 polymorphism information content and 1.35% null alleles. All the 31 ReG-SSR loci were found selectively neutral and showed no evidence of population reduction. A model-based clustering analysis separated the flax accessions into two sub-populations-Indian and global, with some accessions showing admixtures. The distinct clustering pattern of the Indian accessions compared to the global accessions, conforms to the principal coordinate analysis, genetic dissimilarity-based unweighted neighbor-joining tree and analysis of molecular variance. Fourteen flax accessions with 99.3% allelic richness were found optimum to adopt in breeding programs. In summary, the genome-wide ReG-SSR markers will serve as a functional marker resource for genetic and phenotypic relationship studies, marker-assisted selections, and provide a basis for selection of accessions from the Indian and global gene pool in fiber flax breeding programs.
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Affiliation(s)
- Dipnarayan Saha
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700121, India.
| | - Rajeev Singh Rana
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700121, India
| | - Shantanab Das
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700121, India.,School of Agriculture and Rural Development, Ramakrishna Mission Vivekananda University, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, 700103, India
| | - Subhojit Datta
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700121, India
| | - Jiban Mitra
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700121, India
| | - Sylvie J Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Frank M You
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
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Soto-Cerda BJ, Cloutier S, Quian R, Gajardo HA, Olivos M, You FM. Genome-Wide Association Analysis of Mucilage and Hull Content in Flax ( Linum usitatissimum L.) Seeds. Int J Mol Sci 2018; 19:ijms19102870. [PMID: 30248911 PMCID: PMC6213135 DOI: 10.3390/ijms19102870] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 01/20/2023] Open
Abstract
New flaxseed cultivars differing in seed mucilage content (MC) with low hull content (HC) represent an attractive option to simultaneously target the food and feed markets. Here, a genome-wide association study (GWAS) was conducted for MC and HC in 200 diverse flaxseed accessions genotyped with 1.7 million single nucleotide polymorphism (SNP) markers. The data obtained for MC and HC indicated a broad phenotypic variation and high (~70%) and a moderate (~49%) narrow sense heritability, respectively. MC and HC did not differ statistically between fiber and oil morphotypes, but yellow-seeded accessions had 2.7% less HC than brown-seeded ones. The genome-wide linkage disequilibrium (LD) decayed to r2 = 0.1 at a physical distance of ~100 kb. Seven and four quantitative trait loci (QTL) were identified for MC and HC, respectively. Promising candidate genes identified include Linum usitatissimum orthologs of the Arabidopsis thaliana genes TRANSPARENT TESTA 8, SUBTILISIN-LIKE SERINE PROTEASE, GALACTUROSYL TRANSFERASE-LIKE 5, MUCILAGE-MODIFIED 4, AGAMOUS-LIKE MADS-BOX PROTEIN AGL62, GLYCOSYL HYDROLASE FAMILY 17, and UDP-GLUCOSE FLAVONOL 3-O-GLUCOSYLTRANSFERASE. These genes have been shown to play a role in mucilage synthesis and release, seed coat development and anthocyanin biosynthesis in A. thaliana. The favorable alleles will be useful in flaxseed breeding towards the goal of achieving the ideal MC and HC composition for food and feed by genomic-based breeding.
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Affiliation(s)
- Braulio J Soto-Cerda
- Agriaquaculture Nutritional Genomic Center (CGNA), Las Heras 350, Temuco 4781158, Chile.
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Rocío Quian
- Agriaquaculture Nutritional Genomic Center (CGNA), Las Heras 350, Temuco 4781158, Chile.
| | - Humberto A Gajardo
- Agriaquaculture Nutritional Genomic Center (CGNA), Las Heras 350, Temuco 4781158, Chile.
| | - Marcos Olivos
- Agriaquaculture Nutritional Genomic Center (CGNA), Las Heras 350, Temuco 4781158, Chile.
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
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Xie D, Dai Z, Yang Z, Tang Q, Sun J, Yang X, Song X, Lu Y, Zhao D, Zhang L, Su J. Genomic variations and association study of agronomic traits in flax. BMC Genomics 2018; 19:512. [PMID: 29969983 PMCID: PMC6029072 DOI: 10.1186/s12864-018-4899-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 06/26/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Flax (Linum usitatissimum. L) is an ancient oilseed and natural fiber crop. It could be divided into three categories by use, namely oil flax, fiber flax and oil-fiber dual purpose (OF). Cultivated flax is widely used in the food and textile industry. It is of great significance to elucidate the genetic characteristics of flax collections for accelerating the process of breeding improvement in this dual purpose crop. With the development of next-generation sequencing, we can use new methods, such as SLAF-seq (specific-locus amplified fragment sequencing), to decode unknown genomes of species. In this study, a high-through sequencing of flax collections using SLAF-seq was conducted. The evolutionary tendency was defined and candidate genes associated with agronomic traits of flax species were identified by Genome-Wide Association Studying (GWAS). RESULTS A flax collection consisting of 224 varieties were sequenced by SLAF-seq. In total, 346,639 SLAF tags were developed from all accessions, with an average sequencing depth of 7.19 for each accession. A total of 584,987 SNPs (single nucleotide polymorphism) with an MAF > 0.05 were identified from these SLAFs. The population structure division and phylogenetic analysis indicated a strong divergence among three kinds of flax groups. The genome-wide variation uncovered that oil flax had the highest genetic diversity and was considered to be the ancestor of fiber flax and oil-fiber flax. Sixteen associated peak SNPs for six traits were obtained by GWAS of oil-related traits using EMMAX (efficient mixed-model association eXpedited). Candidate genes and their related pathway were evaluated. A new GWAS was developed for fiber properties using the GLM (General linear model) model and a number of loci were identified. CONCLUSIONS To our knowledge, this is the first study on discovery multiple loci for important agronomic traits of flax species using GWAS strategy. These results will provide the highest possibility of incorporating both high fiber and good oil traits in a single variety.
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Affiliation(s)
- Dongwei Xie
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- The Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jian Sun
- Agricultural College, Northeast Agricultural University, Harbin, China
| | - Xue Yang
- Sino-Russian Agricultural Scientific and Technological Cooperation Center, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xixia Song
- The Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Ying Lu
- The Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Debao Zhao
- The Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Liguo Zhang
- The Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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24
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Xie D, Dai Z, Yang Z, Tang Q, Sun J, Yang X, Song X, Lu Y, Zhao D, Zhang L, Su J. Genomic variations and association study of agronomic traits in flax. BMC Genomics 2018. [PMID: 29969983 DOI: 10.1186/s12864-018-4899-za] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
BACKGROUND Flax (Linum usitatissimum. L) is an ancient oilseed and natural fiber crop. It could be divided into three categories by use, namely oil flax, fiber flax and oil-fiber dual purpose (OF). Cultivated flax is widely used in the food and textile industry. It is of great significance to elucidate the genetic characteristics of flax collections for accelerating the process of breeding improvement in this dual purpose crop. With the development of next-generation sequencing, we can use new methods, such as SLAF-seq (specific-locus amplified fragment sequencing), to decode unknown genomes of species. In this study, a high-through sequencing of flax collections using SLAF-seq was conducted. The evolutionary tendency was defined and candidate genes associated with agronomic traits of flax species were identified by Genome-Wide Association Studying (GWAS). RESULTS A flax collection consisting of 224 varieties were sequenced by SLAF-seq. In total, 346,639 SLAF tags were developed from all accessions, with an average sequencing depth of 7.19 for each accession. A total of 584,987 SNPs (single nucleotide polymorphism) with an MAF > 0.05 were identified from these SLAFs. The population structure division and phylogenetic analysis indicated a strong divergence among three kinds of flax groups. The genome-wide variation uncovered that oil flax had the highest genetic diversity and was considered to be the ancestor of fiber flax and oil-fiber flax. Sixteen associated peak SNPs for six traits were obtained by GWAS of oil-related traits using EMMAX (efficient mixed-model association eXpedited). Candidate genes and their related pathway were evaluated. A new GWAS was developed for fiber properties using the GLM (General linear model) model and a number of loci were identified. CONCLUSIONS To our knowledge, this is the first study on discovery multiple loci for important agronomic traits of flax species using GWAS strategy. These results will provide the highest possibility of incorporating both high fiber and good oil traits in a single variety.
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Affiliation(s)
- Dongwei Xie
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- The Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jian Sun
- Agricultural College, Northeast Agricultural University, Harbin, China
| | - Xue Yang
- Sino-Russian Agricultural Scientific and Technological Cooperation Center, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xixia Song
- The Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Ying Lu
- The Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Debao Zhao
- The Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Liguo Zhang
- The Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.
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Burnett PGG, Young LW, Olivia CM, Jadhav PD, Okinyo-Owiti DP, Reaney MJT. Novel flax orbitide derived from genetic deletion. BMC PLANT BIOLOGY 2018; 18:90. [PMID: 29783946 PMCID: PMC5963108 DOI: 10.1186/s12870-018-1303-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 04/30/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Flaxseed orbitides are homodetic plant cyclic peptides arising from ribosomal synthesis and post-translation modification (N to C cyclization), and lacking cysteine double bonds (Nat Prod Rep 30:108-160, 2013). Screening for orbitide composition was conducted on the flax core collection (FCC) grown at both Saskatoon, Saskatchewan and Morden, Manitoba over three growing seasons (2009-2011). Two flax (Linum usitatissimum L.) accessions 'Hollandia' (CN 98056) and 'Z 11637' (CN 98150) produce neither [1-9-NαC]-linusorb B2 (3) nor [1-9-NαC]-linusorb B3 (1). Mass spectrometry was used to identify novel compounds and elucidate their structure. NMR spectroscopy was used to corroborate structural information. RESULTS Experimental findings indicated that these accessions produce a novel orbitide, identified in three oxidation states having quasimolecular ion peaks at m/z 1072.6 (18), 1088.6 (19), and 1104.6 (20) [M + H]+ corresponding to molecular formulae C57H86N9O9S, C57H86N9O10S, and C57H86N9O11S, respectively. The structure of 19 was confirmed unequivocally as [1-9-NαC]-OLIPPFFLI. PCR amplification and sequencing of the gene coding for 18, using primers developed for 3 and 1, identified the putative linear precursor protein of 18 as being comprised of the first three amino acid residues of 3 (MLI), four conserved amino acid residues of 3 and/or 1 (PPFF), and the last two residues of 1 (LI). CONCLUSION Comparison of gene sequencing data revealed that a 117 base pair deletion had occurred that resulted in truncation of both 3 and 1 to produce a sequence encoding for the novel orbitide precursor of 18. This observation suggests that repeat units of flax orbitide genes are conserved and suggests a novel mechanism for evolution of orbitide gene diversity. Orbitides 19 and 20 contain MetO and MetO2, respectively, and are not directly encoded, but are products of post-translation modification of Met present in 18 ([1-9-NαC]-MLIPPFFLI).
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Affiliation(s)
- Peta-Gaye Gillian Burnett
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada
| | - Lester Warren Young
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada
| | - Clara Marisa Olivia
- Department of Food and Bioproduct Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada
| | - Pramodkumar Dinkar Jadhav
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada
| | - Denis Paskal Okinyo-Owiti
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada
| | - Martin John Tarsisius Reaney
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8 Canada
- Guangdong Saskatchewan Oilseed Joint Laboratory, Department of Food Science and Engineering, Jinan University, Guangzhou, 510632 Guangdong China
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Duan H, Cao S, Zheng H, Hu D, Lin J, Cui B, Lin H, Hu R, Wu B, Sun Y, Li Y. Genetic Characterization of Chinese fir from Six Provinces in Southern China and Construction of a Core Collection. Sci Rep 2017; 7:13814. [PMID: 29062029 PMCID: PMC5653812 DOI: 10.1038/s41598-017-13219-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 09/20/2017] [Indexed: 12/03/2022] Open
Abstract
Large ex situ germplasm collections of plants generally contain significant diversity. A set of 700 well-conserved Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) clones from six provinces in southern China in the ex situ gene bank of Longshan State Forest, was analyzed using 21 simple sequence repeat markers, with the aim of assessing the genetic diversity of these germplasm resources. Genetic analysis revealed extensive genetic variation among the accessions, with an average of 8.31 alleles per locus and a mean Shannon index of 1.331. Excluding loci with null alleles, we obtained a low level of genetic differentiation among provinces, consistent with the interpopulation genetic variation (1%). Three clusters were identified by STRUCTURE, which did not match the individuals’ geographical provenances. Ten traits related to growth and wood properties were quantified in these individuals, and there was substantial variation in all traits across individuals, these provide a potential source of variation for genetic improvement of the Chinese fir. Screening large collections for multiple-trait selective breeding programs is laborious and expensive; a core collection of 300 accessions, representative of the germplasm, was established, based on genotypic and phenotypic data. The identified small, but diverse, collections will be useful for further genome-wide association studies.
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Affiliation(s)
- Hongjing Duan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design. National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, 100083, Beijing, People's Republic of China
| | - Sen Cao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design. National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, 100083, Beijing, People's Republic of China
| | - Huiquan Zheng
- Guangdong Provincial Key Laboratory of Bio-control for the Forest Disease and Pest, Guangdong Academy of Forestry, 510520, Guangzhou, People's Republic of China
| | - Dehuo Hu
- Guangdong Provincial Key Laboratory of Bio-control for the Forest Disease and Pest, Guangdong Academy of Forestry, 510520, Guangzhou, People's Republic of China
| | - Jun Lin
- The ex situ gene bank of Longshan State Forest Farm, 512221, Guangzhou, Guangdong Province, People's Republic of China
| | - Binbin Cui
- Department of Biochemistry, Baoding University, 071000, Baoding, Hebei Province, People's Republic of China
| | - Huazhong Lin
- Fujian Jiangle State-owned Forestry Farm, Fujian, 353300, China
| | - Ruiyang Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design. National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, 100083, Beijing, People's Republic of China
| | - Bo Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design. National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, 100083, Beijing, People's Republic of China
| | - Yuhan Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design. National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, 100083, Beijing, People's Republic of China
| | - Yun Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design. National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, 100083, Beijing, People's Republic of China.
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You FM, Jia G, Xiao J, Duguid SD, Rashid KY, Booker HM, Cloutier S. Genetic Variability of 27 Traits in a Core Collection of Flax ( Linum usitatissimum L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1636. [PMID: 28993783 PMCID: PMC5622609 DOI: 10.3389/fpls.2017.01636] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/06/2017] [Indexed: 05/20/2023]
Abstract
Assessment of genetic variability of plant core germplasm is needed for efficient germplasm utilization in breeding improvement. A total of 391 accessions of a flax core collection, which preserves the variation present in the world collection of 3,378 accessions maintained by Plant Gene Resources of Canada (PGRC) and represents a broad range of geographical origins, different improvement statuses and two morphotypes, was evaluated in field trials in up to 8 year-location environments for 10 agronomic, eight seed quality, six fiber and three disease resistance traits. The large phenotypic variation in this subset was explained by morphotypes (22%), geographical origins (11%), and other variance components (67%). Both divergence and similarity between two basic morphotypes, namely oil or linseed and fiber types, were observed, whereby linseed accessions had greater thousand seed weight, seeds m-2, oil content, branching capability and resistance to powdery mildew while fiber accessions had greater straw weight, plant height, protein content and resistance to pasmo and fusarium wilt diseases, but they had similar performance in many traits and some of them shared common characteristics of fiber and linseed types. Weak geographical patterns within either fiber or linseed accessions were confirmed, but specific trait performance was identified in East Asia for fiber type, and South Asia and North America for linseed type. Relatively high broad-sense heritability was obtained for seed quality traits, followed by agronomic traits and resistance to powdery mildew and fusarium wilt. Diverse phenotypic and genetic variability in the flax core collection constitutes a useful resource for breeding.
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Affiliation(s)
- Frank M. You
- Morden Research and Development Centre, Agriculture and Agri-Food CanadaMorden, MB, Canada
- *Correspondence: Frank M. You
| | - Gaofeng Jia
- Morden Research and Development Centre, Agriculture and Agri-Food CanadaMorden, MB, Canada
- Crop Development Centre, Department of Plant Sciences, University of SaskatchewanSaskatoon, SK, Canada
| | - Jin Xiao
- Morden Research and Development Centre, Agriculture and Agri-Food CanadaMorden, MB, Canada
- Department of Agronomy, Nanjing Agricultural UniversityNanjing, China
| | - Scott D. Duguid
- Morden Research and Development Centre, Agriculture and Agri-Food CanadaMorden, MB, Canada
| | - Khalid Y. Rashid
- Morden Research and Development Centre, Agriculture and Agri-Food CanadaMorden, MB, Canada
| | - Helen M. Booker
- Crop Development Centre, Department of Plant Sciences, University of SaskatchewanSaskatoon, SK, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food CanadaOttawa, ON, Canada
- Sylvie Cloutier
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Singh N, Kumar R, Kumar S, Singh PK, Yadav VK, Ranade SA, Yadav HK. Genetic diversity, population structure and association analysis in linseed ( Linum usitatissimum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:207-219. [PMID: 28250596 PMCID: PMC5313412 DOI: 10.1007/s12298-016-0408-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/15/2016] [Accepted: 12/23/2016] [Indexed: 05/16/2023]
Abstract
The present investigation aimed to explore the level of genetic diversity, determine the population structure in a larger set of germplasm of linseed using microsatellite marker and identify linked markers through association mapping. A total of 168 accessions of linseed were evaluated for major agro-economic traits and SSRs markers deployed for diversity assessment. A total of 337 alleles were amplified by 50 SSRs ranging from 2 to 13 with an average of 6.74 ± 2.8 alleles per loci. The neighbor joining based clustering grouped all the accessions into three major clusters that were also confirmed by scatter plot of PCoA. While model based clustering determined four sub-populations (K = 4). Further, analysis of molecular variance analysis considering three population showed that maximum variation (79%) was within the population. We identified one putative SSR marker (Lu_3043) linked with days to 50% flowering through both GLM and MLM analysis of association mapping. The results of this preliminary study revealed genetic diversity, population structure in linseed and linked marker which could be utilized in future breeding program.
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Affiliation(s)
- Neha Singh
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226001 India
| | - Rajendra Kumar
- Uttar Pradesh Council of Agricultural Research (UPCAR), Vibhuti Khand, Gomatinagar, Lucknow, 226010 India
| | - Sujit Kumar
- Uttar Pradesh Council of Agricultural Research (UPCAR), Vibhuti Khand, Gomatinagar, Lucknow, 226010 India
| | | | - V. K. Yadav
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226001 India
- Academy of Scientific and Innovative Research, New Delhi, India
| | - S. A. Ranade
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226001 India
| | - Hemant Kumar Yadav
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, UP 226001 India
- Academy of Scientific and Innovative Research, New Delhi, India
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Xie D, Dai Z, Yang Z, Sun J, Zhao D, Yang X, Zhang L, Tang Q, Su J. Genome-Wide Association Study Identifying Candidate Genes Influencing Important Agronomic Traits of Flax ( Linum usitatissimum L.) Using SLAF-seq. FRONTIERS IN PLANT SCIENCE 2017; 8:2232. [PMID: 29375606 PMCID: PMC5767239 DOI: 10.3389/fpls.2017.02232] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 12/19/2017] [Indexed: 05/13/2023]
Abstract
Flax (Linum usitatissimum L.) is an important cash crop, and its agronomic traits directly affect yield and quality. Molecular studies on flax remain inadequate because relatively few flax genes have been associated with agronomic traits or have been identified as having potential applications. To identify markers and candidate genes that can potentially be used for genetic improvement of crucial agronomic traits, we examined 224 specimens of core flax germplasm; specifically, phenotypic data for key traits, including plant height, technical length, number of branches, number of fruits, and 1000-grain weight were investigated under three environmental conditions before specific-locus amplified fragment sequencing (SLAF-seq) was employed to perform a genome-wide association study (GWAS) for these five agronomic traits. Subsequently, the results were used to screen single nucleotide polymorphism (SNP) loci and candidate genes that exhibited a significant correlation with the important agronomic traits. Our analyses identified a total of 42 SNP loci that showed significant correlations with the five important agronomic flax traits. Next, candidate genes were screened in the 10 kb zone of each of the 42 SNP loci. These SNP loci were then analyzed by a more stringent screening via co-identification using both a general linear model (GLM) and a mixed linear model (MLM) as well as co-occurrences in at least two of the three environments, whereby 15 final candidate genes were obtained. Based on these results, we determined that UGT and PL are candidate genes for plant height, GRAS and XTH are candidate genes for the number of branches, Contig1437 and LU0019C12 are candidate genes for the number of fruits, and PHO1 is a candidate gene for the 1000-seed weight. We propose that the identified SNP loci and corresponding candidate genes might serve as a biological basis for improving crucial agronomic flax traits.
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Affiliation(s)
- Dongwei Xie
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jian Sun
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Debao Zhao
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xue Yang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Liguo Zhang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- *Correspondence: Jianguang Su
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Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions. BMC Genomics 2016; 17:1002. [PMID: 27927184 PMCID: PMC5142383 DOI: 10.1186/s12864-016-3337-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/23/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Initial characterization of the flax genome showed that Ty1-copia retrotransposons are abundant, with several members being recently inserted, and in close association with genes. Recent insertions indicate a potential for ongoing transpositional activity that can create genomic diversity among accessions, cultivars or varieties. The polymorphisms generated constitute a good source of molecular markers that may be associated with phenotype if the insertions alter gene activity. Flax, where accessions are bred mainly for seed nutritional properties or for fibers, constitutes a good model for studying the relationship of transpositional activity with diversification and breeding. In this study, we estimated copy number and used a type of transposon display known as Sequence-Specific Amplification Polymorphisms (SSAPs), to characterize six families of Ty1-copia elements across 14 flax accessions. Polymorphic insertion sites were sequenced to find insertions that could potentially alter gene expression, and a preliminary test was performed with selected genes bearing transposable element (TE) insertions. RESULTS Quantification of six families of Ty1-copia elements indicated different abundances among TE families and between flax accessions, which suggested diverse transpositional histories. SSAPs showed a high level of polymorphism in most of the evaluated retrotransposon families, with a trend towards higher levels of polymorphism in low-copy number families. Ty1-copia insertion polymorphisms among cultivars allowed a general distinction between oil and fiber types, and between spring and winter types, demonstrating their utility in diversity studies. Characterization of polymorphic insertions revealed an overwhelming association with genes, with insertions disrupting exons, introns or within 1 kb of coding regions. A preliminary test on the potential transcriptional disruption by TEs of four selected genes evaluated in three different tissues, showed one case of significant impact of the insertion on gene expression. CONCLUSIONS We demonstrated that specific Ty1-copia families have been active since breeding commenced in flax. The retrotransposon-derived polymorphism can be used to separate flax types, and the close association of many insertions with genes defines a good source of potential mutations that could be associated with phenotypic changes, resulting in diversification processes.
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Roy Choudhury D, Singh N, Singh AK, Kumar S, Srinivasan K, Tyagi RK, Ahmad A, Singh NK, Singh R. Analysis of genetic diversity and population structure of rice germplasm from north-eastern region of India and development of a core germplasm set. PLoS One 2014; 9:e113094. [PMID: 25412256 PMCID: PMC4239046 DOI: 10.1371/journal.pone.0113094] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/18/2014] [Indexed: 11/30/2022] Open
Abstract
The North-Eastern region (NER) of India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland and Tripura, is a hot spot for genetic diversity and the most probable origin of rice. North-east rice collections are known to possess various agronomically important traits like biotic and abiotic stress tolerance, unique grain and cooking quality. The genetic diversity and associated population structure of 6,984 rice accessions, originating from NER, were assessed using 36 genome wide unlinked single nucleotide polymorphism (SNP) markers distributed across the 12 rice chromosomes. All of the 36 SNP loci were polymorphic and bi-allelic, contained five types of base substitutions and together produced nine types of alleles. The polymorphic information content (PIC) ranged from 0.004 for Tripura to 0.375 for Manipur and major allele frequency ranged from 0.50 for Assam to 0.99 for Tripura. Heterozygosity ranged from 0.002 in Nagaland to 0.42 in Mizoram and gene diversity ranged from 0.006 in Arunachal Pradesh to 0.50 in Manipur. The genetic relatedness among the rice accessions was evaluated using an unrooted phylogenetic tree analysis, which grouped all accessions into three major clusters. For determining population structure, populations K = 1 to K = 20 were tested and population K = 3 was present in all the states, with the exception of Meghalaya and Manipur where, K = 5 and K = 4 populations were present, respectively. Principal Coordinate Analysis (PCoA) showed that accessions were distributed according to their population structure. AMOVA analysis showed that, maximum diversity was partitioned at the individual accession level (73% for Nagaland, 58% for Arunachal Pradesh and 57% for Tripura). Using POWERCORE software, a core set of 701 accessions was obtained, which accounted for approximately 10% of the total NE India collections, representing 99.9% of the allelic diversity. The rice core set developed will be a valuable resource for future genomic studies and crop improvement strategies.
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Affiliation(s)
- Debjani Roy Choudhury
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Nivedita Singh
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Amit Kumar Singh
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Sundeep Kumar
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Kalyani Srinivasan
- Division of Germplasm Conservation, National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - R. K. Tyagi
- Division of Germplasm Conservation, National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
| | - Altaf Ahmad
- Department of Botany, Faculty of Science, Jamia Hamdard (Hamdard University), New Delhi, 110062, India
| | - N. K. Singh
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Rakesh Singh
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi, 110 012, India
- * E-mail:
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Soto-Cerda BJ, Diederichsen A, Duguid S, Booker H, Rowland G, Cloutier S. The potential of pale flax as a source of useful genetic variation for cultivated flax revealed through molecular diversity and association analyses. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 34:2091-2107. [PMID: 26316841 PMCID: PMC4544635 DOI: 10.1007/s11032-014-0165-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/29/2014] [Indexed: 05/25/2023]
Abstract
Pale flax (Linum bienne Mill.) is the wild progenitor of cultivated flax (Linum usitatissimum L.) and represents the primary gene pool to broaden its genetic base. Here, a collection of 125 pale flax accessions and the Canadian flax core collection of 407 accessions were genotyped using 112 genome-wide simple sequence repeat markers and phenotyped for nine traits with the aim of conducting population structure, molecular diversity and association mapping analyses. The combined population structure analysis identified two well-supported major groups corresponding to pale and cultivated flax. The L. usitatissimum convar. crepitans accessions most closely resembled its wild progenitor, both having dehiscent capsules. The unbiased Nei's genetic distance (0.65) confirmed the strong genetic differentiation between cultivated and pale flax. Similar levels of genetic diversity were observed in both species, albeit 430 (48 %) of pale flax alleles were unique, in agreement with their high genetic differentiation. Significant associations were identified for seven and four traits in pale and cultivated flax, respectively. Favorable alleles with potentially positive effect to improve yield through yield components were identified in pale flax. The allelic frequencies of markers associated with domestication-related traits such as capsular dehiscence indicated directional selection with the most common alleles in pale flax being absent or rare in cultivated flax and vice versa. Our results demonstrated that pale flax is a potential source of novel variation to improve multiple traits in cultivated flax and that association mapping is a suitable approach to screening pale flax germplasm to identify favorable quantitative trait locus alleles.
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Affiliation(s)
- Braulio J. Soto-Cerda
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9 Canada
- Present Address: Agriaquaculture Nutritional Genomic Center, CGNA, Genomics and Bioinformatics Unit, 4791057 Temuco, Chile
| | - Axel Diederichsen
- Plant Gene Resources of Canada, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Scott Duguid
- Morden Research Station, Agriculture and Agri-Food Canada, 101 Route 100, Unit 100, Morden, MB R6M 1Y5 Canada
| | - Helen Booker
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Gordon Rowland
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Sylvie Cloutier
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9 Canada
- Present Address: Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON K1A 0C6 Canada
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Bolibok-Brągoszewska H, Targońska M, Bolibok L, Kilian A, Rakoczy-Trojanowska M. Genome-wide characterization of genetic diversity and population structure in Secale. BMC PLANT BIOLOGY 2014; 14:184. [PMID: 25085433 PMCID: PMC4236688 DOI: 10.1186/1471-2229-14-184] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/27/2014] [Indexed: 05/02/2023]
Abstract
BACKGROUND Numerous rye accessions are stored in ex situ genebanks worldwide. Little is known about the extent of genetic diversity contained in any of them and its relation to contemporary varieties, since to date rye genetic diversity studies had a very limited scope, analyzing few loci and/ or few accessions. Development of high throughput genotyping methods for rye opened the possibility for genome wide characterizations of large accessions sets. In this study we used 1054 Diversity Array Technology (DArT) markers with defined chromosomal location to characterize genetic diversity and population structure in a collection of 379 rye accessions including wild species, landraces, cultivated materials, historical and contemporary rye varieties. RESULTS Average genetic similarity (GS) coefficients and average polymorphic information content (PIC) values varied among chromosomes. Comparison of chromosome specific average GS within and between germplasm sub-groups indicated regions of chromosomes 1R and 4R as being targeted by selection in current breeding programs. Bayesian clustering, principal coordinate analysis and Neighbor Joining clustering demonstrated that source and improvement status contributed significantly to the structure observed in the analyzed set of Secale germplasm. We revealed a relatively limited diversity in improved rye accessions, both historical and contemporary, as well as lack of correlation between clustering of improved accessions and geographic origin, suggesting common genetic background of rye accessions from diverse geographic regions and extensive germplasm exchange. Moreover, contemporary varieties were distinct from the remaining accessions. CONCLUSIONS Our results point to an influence of reproduction methods on the observed diversity patterns and indicate potential of ex situ collections for broadening the genetic diversity in rye breeding programs. Obtained data show that DArT markers provide a realistic picture of the genetic diversity and population structure present in the collection of 379 rye accessions and are an effective platform for rye germplasm characterization and association mapping studies.
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Affiliation(s)
- Hanna Bolibok-Brągoszewska
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
| | - Małgorzata Targońska
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
| | - Leszek Bolibok
- Department of Silviculture, Faculty of Forestry, Warsaw University of Life Sciences, Warsaw, Poland
| | - Andrzej Kilian
- Diversity Arrays Technology Pty. Ltd, Yarralumla ACT, Australia
| | - Monika Rakoczy-Trojanowska
- Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland
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Gepts P. The contribution of genetic and genomic approaches to plant domestication studies. CURRENT OPINION IN PLANT BIOLOGY 2014; 18:51-9. [PMID: 24631844 DOI: 10.1016/j.pbi.2014.02.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/04/2014] [Accepted: 02/09/2014] [Indexed: 05/25/2023]
Abstract
The application of genomic approaches to the phenomenon of plant domestication promises a better understanding of the origins of agriculture, but also of the way plant genomes in general are organized and expressed. Building on earlier genetic research, more detailed information has become available on the organization of genetic diversity at the genome level and the effects of gene flow on diversity in different regions of the genome. In addition, putative domestication genes have been identified through population genomics approaches (selective sweeps or divergence scanning). Further information has been obtained on the origin of domestication syndrome mutations and the dispersal and adaptation of crops after domestication. For the future, increasingly multidisciplinary approaches using combinations of genomics and other approaches will prevail.
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Affiliation(s)
- Paul Gepts
- University of California, Department of Plant Sciences/MS 1, Section of Crop and Ecosystem Sciences, 1 Shields Avenue, Davis, CA 95616, United States of America.
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Soto-Cerda BJ, Duguid S, Booker H, Rowland G, Diederichsen A, Cloutier S. Association mapping of seed quality traits using the Canadian flax (Linum usitatissimum L.) core collection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:881-96. [PMID: 24463785 PMCID: PMC3964306 DOI: 10.1007/s00122-014-2264-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 01/03/2014] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE The identification of stable QTL for seed quality traits by association mapping of a diverse panel of linseed accessions establishes the foundation for assisted breeding and future fine mapping in linseed. Linseed oil is valued for its food and non-food applications. Modifying its oil content and fatty acid (FA) profiles to meet market needs in a timely manner requires clear understanding of their quantitative trait loci (QTL) architectures, which have received little attention to date. Association mapping is an efficient approach to identify QTL in germplasm collections. In this study, we explored the quantitative nature of seed quality traits including oil content (OIL), palmitic acid, stearic acid, oleic acid, linoleic acid (LIO) linolenic acid (LIN) and iodine value in a flax core collection of 390 accessions assayed with 460 microsatellite markers. The core collection was grown in a modified augmented design at two locations over 3 years and phenotypic data for all seven traits were obtained from all six environments. Significant phenotypic diversity and moderate to high heritability for each trait (0.73-0.99) were observed. Most of the candidate QTL were stable as revealed by multivariate analyses. Nine candidate QTL were identified, varying from one for OIL to three for LIO and LIN. Candidate QTL for LIO and LIN co-localized with QTL previously identified in bi-parental populations and some mapped nearby genes known to be involved in the FA biosynthesis pathway. Fifty-eight percent of the QTL alleles were absent (private) in the Canadian cultivars suggesting that the core collection possesses QTL alleles potentially useful to improve seed quality traits. The candidate QTL identified herein will establish the foundation for future marker-assisted breeding in linseed.
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Affiliation(s)
- Braulio J. Soto-Cerda
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2 Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9 Canada
- Genomics and Bioinformatics Unit, Agriaquaculture Nutritional Genomic Center (CGNA), Km 10 Camino Cajón-Vilcún, Temuco, La Araucania Chile
| | - Scott Duguid
- Morden Research Station, Agriculture and Agri-Food Canada, Route 100, Morden, MB R6M 1Y5 Canada
| | - Helen Booker
- Crop Development Centre, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Gordon Rowland
- Crop Development Centre, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Axel Diederichsen
- Plant Gene Resources of Canada, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Sylvie Cloutier
- Department of Plant Science, University of Manitoba, 66 Dafoe Road, Winnipeg, MB R3T 2N2 Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, MB R3T 2M9 Canada
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Soto-Cerda BJ, Duguid S, Booker H, Rowland G, Diederichsen A, Cloutier S. Genomic regions underlying agronomic traits in linseed (Linum usitatissimum L.) as revealed by association mapping. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:75-87. [PMID: 24138336 PMCID: PMC4253320 DOI: 10.1111/jipb.12118] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/13/2013] [Indexed: 05/20/2023]
Abstract
The extreme climate of the Canadian Prairies poses a major challenge to improve yield. Although it is possible to breed for yield per se, focusing on yield-related traits could be advantageous because of their simpler genetic architecture. The Canadian flax core collection of 390 accessions was genotyped with 464 simple sequence repeat markers, and phenotypic data for nine agronomic traits including yield, bolls per area, 1,000 seed weight, seeds per boll, start of flowering, end of flowering, plant height, plant branching, and lodging collected from up to eight environments was used for association mapping. Based on a mixed model (principal component analysis (PCA) + kinship matrix (K)), 12 significant marker-trait associations for six agronomic traits were identified. Most of the associations were stable across environments as revealed by multivariate analyses. Statistical simulation for five markers associated with 1000 seed weight indicated that the favorable alleles have additive effects. None of the modern cultivars carried the five favorable alleles and the maximum number of four observed in any accessions was mostly in breeding lines. Our results confirmed the complex genetic architecture of yield-related traits and the inherent difficulties associated with their identification while illustrating the potential for improvement through marker-assisted selection.
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Affiliation(s)
- Braulio J Soto-Cerda
- Department of Plant Science, University of Manitoba66 Dafoe Road, Winnipeg, Manitoba, R3T 2N2, Canada
- Cereal Research Center, Agriculture and Agri-Food Canada195 Dafoe Road, Winnipeg, Manitoba, R3T 2M9, Canada
- † Permanent address: Agriaquaculture Nutritional Genomic Center, CGNA, Genomics and Bioinformatics Unit, Km 10 Camino Cajón-Vilcún, INIA, Temuco, Chile
| | - Scott Duguid
- Morden Research Station, Agriculture and Agri-Food Canada101 Route 100, Unit 100 Morden, Manitoba, R6M 1Y5, Canada
| | - Helen Booker
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan51 Campus Drive, Saskatoon, Saskatchewan, S7N 5A8, Canada
| | - Gordon Rowland
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan51 Campus Drive, Saskatoon, Saskatchewan, S7N 5A8, Canada
| | - Axel Diederichsen
- Plant Gene Resources of Canada, Agriculture and Agri-Food Canada107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Sylvie Cloutier
- Department of Plant Science, University of Manitoba66 Dafoe Road, Winnipeg, Manitoba, R3T 2N2, Canada
- Cereal Research Center, Agriculture and Agri-Food Canada195 Dafoe Road, Winnipeg, Manitoba, R3T 2M9, Canada
- * Correspondence:
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